Merge branch 'mixed-env-with-zlib' of https://github.com/sbmlteam/lib…

…sbml into mixed-env-with-zlib
sbmlteam · May 5, 2023 · f16490f · f16490f
2 parents f6ac408 + b70acac
commit f16490f
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diff --git a/src/sbml/packages/comp/util/CompFlatteningConverter.cpp b/src/sbml/packages/comp/util/CompFlatteningConverter.cpp
@@ -385,6 +385,8 @@ CompFlatteningConverter::performConversion()
     mDocument->getVersion(),
     "The subsequent errors are from this attempt.");
 
+  unsetExplicitlyListed();
+
   // setup callback that will enable the packages on submodels
   disable_info mainDoc;
   mainDoc.doc = mDocument;
@@ -1253,6 +1255,19 @@ CompFlatteningConverter::restoreNamespaces()
     mDocument->enablePackage((*pkg).first, (*pkg).second, true);
   }
 }
+
+void CompFlatteningConverter::unsetExplicitlyListed()
+{
+    List* elements = mDocument->getAllElements();
+    for (unsigned int el = 0; el < elements->getSize(); el++) {
+        SBase* element = static_cast<SBase*>(elements->get(el));
+        if (element->getTypeCode() == SBML_LIST_OF) {
+            ListOf* lo = static_cast<ListOf*>(element);
+            lo->setExplicitlyListed(false);
+        }
+    }
+}
+
 /** @endcond */
 
 /** @cond doxygenLibsbmlInternal */

diff --git a/src/sbml/packages/comp/util/CompFlatteningConverter.h b/src/sbml/packages/comp/util/CompFlatteningConverter.h
@@ -656,6 +656,8 @@ class LIBSBML_EXTERN CompFlatteningConverter : public SBMLConverter
 
   void restoreNamespaces();
 
+  void unsetExplicitlyListed();
+
   std::set<std::pair<std::string, std::string> > mDisabledPackages;
 
 #ifndef SWIG

diff --git a/src/sbml/util/ElementFilter.h b/src/sbml/util/ElementFilter.h
@@ -87,6 +87,10 @@ LIBSBML_CPP_NAMESPACE_BEGIN
     pResult->transferFrom(pSublist);\
     delete pSublist;\
   }\
+  else {\
+    if ((pFilter == NULL || pFilter->filter(&list)) && list.getLevel() >= 3 && list.getVersion() >= 2 && list.isExplicitlyListed())\
+    pResult->add(&list);\
+  }\
 }
 
 #define ADD_FILTERED_PLIST(pResult,pSublist,pList,pFilter)\